Contacts of the strand formed by residues 320 - 333 (chain B) in PDB entry 1AF6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TRP* 6.2 3.8 - - + -
316B TRP* 3.2 37.5 + - + -
317B THR* 3.1 30.0 + - + +
319B ILE* 1.3 80.7 - - + +
321B SER* 1.3 66.7 + - - +
349B GLN* 3.8 22.4 - - - +
350B GLN 3.3 8.5 - - - +
351B TRP* 3.7 35.7 - - + +
352B GLN* 4.7 0.2 - - - -
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B MET* 3.1 33.2 - - - +
314B TYR 3.2 16.2 - - - -
315B LYS* 4.1 2.2 - - - -
316B TRP* 3.9 5.6 - - - -
320B MET* 1.3 77.1 - - - +
322B THR* 1.3 62.4 + - - +
323B VAL* 3.8 3.7 - - - +
349B GLN* 3.4 8.7 - - - -
350B GLN* 2.8 40.0 + - - +
352B GLN* 2.9 20.4 + - - -
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO 4.2 0.5 - - - +
313B MET* 3.5 2.4 - - - +
314B TYR* 2.8 40.8 + - + +
316B TRP* 2.8 28.3 + - + -
321B SER* 1.3 71.1 - - - +
323B VAL* 1.3 64.1 + - - +
324B MET* 5.8 0.9 - - + -
347B LEU* 4.0 22.7 - - + -
348B ALA 3.4 9.9 - - - +
349B GLN* 2.5 23.2 + - - +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.0 17.2 - - + +
311B ARG* 3.8 25.4 - - + +
312B PRO 3.7 11.7 - - - +
313B MET* 3.9 14.6 - - + -
321B SER* 3.8 17.5 - - - +
322B THR* 1.3 80.1 - - - +
324B MET* 1.3 65.3 + - - +
347B LEU* 3.6 2.6 - - - +
348B ALA* 2.7 47.4 + - + +
350B GLN* 3.9 28.5 - - + +
357B ILE* 5.2 3.4 - - + -
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.6 0.9 - - - -
311B ARG* 3.2 10.7 - - - +
312B PRO* 3.1 43.4 + - + +
322B THR* 5.8 0.9 - - + -
323B VAL* 1.3 77.8 - - - +
325B GLU* 1.3 65.3 + - - +
326B ILE* 4.1 29.2 - - + -
345B ILE* 5.2 8.3 - - + -
346B THR 3.2 11.0 - - - +
347B LEU* 3.9 26.5 - - + -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.4 20.4 - - + +
33B ARG 4.3 0.2 - - - -
34B LEU* 3.0 29.0 + - + +
114B MET* 3.6 20.5 - - + +
310B ILE 3.5 9.9 - - - +
311B ARG* 2.9 36.9 + - - -
324B MET* 1.3 76.0 - - - +
326B ILE* 1.3 67.7 + - - +
344B LYS* 2.7 32.6 + - - +
345B ILE* 3.4 4.3 - - - +
346B THR* 2.8 39.7 + - - +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 4.6 0.7 - - - -
309B GLY* 3.0 4.7 - - - -
310B ILE* 2.9 58.4 + - + +
324B MET* 4.1 26.2 - - + -
325B GLU* 1.3 81.0 - - - +
327B GLY* 1.3 63.4 + - - +
328B TYR* 6.3 0.7 - - + -
343B TYR* 5.8 4.5 - - + -
344B LYS 3.4 8.5 - - - +
345B ILE* 4.4 19.1 - - + -
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.6 31.8 - - - +
308B VAL 3.6 5.8 - - - -
325B GLU 4.2 0.4 - - - -
326B ILE* 1.3 77.6 - - - +
328B TYR* 1.3 60.7 + - - +
329B ASP* 5.2 0.6 - - - +
342B GLN 3.9 0.3 - - - +
343B TYR* 3.2 4.4 - - - +
344B LYS* 2.8 39.9 + - - +
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Residues in contact with TYR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TYR* 3.8 1.0 - - - -
306B TRP* 5.0 5.8 - - + -
307B THR* 3.2 10.0 - - - +
308B VAL* 2.8 53.1 + - + +
326B ILE* 6.3 0.9 - - + -
327B GLY* 1.3 75.5 - - - +
329B ASP* 1.3 69.1 + - - +
330B ASN* 3.3 42.0 + - + +
341B ASN* 4.0 15.2 - - + +
342B GLN 3.3 16.4 - - - -
343B TYR* 4.2 13.9 - + + -
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Residues in contact with ASP 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 5.9 0.2 - - - -
25B THR* 3.3 34.2 + - + +
28B ALA* 4.2 3.8 - - - +
30B SER* 4.5 9.0 + - - +
31B LYS* 5.1 2.3 - - - -
32B TYR* 3.9 15.9 - - - -
305B TRP* 3.3 17.8 + - - +
306B TRP 3.6 3.4 - - - -
307B THR* 2.7 29.9 - - - +
327B GLY 5.2 0.5 - - - +
328B TYR* 1.3 78.2 - - - +
330B ASN* 1.3 61.4 + - - +
340B ASN 4.4 0.2 - - - -
341B ASN* 3.1 7.4 - - - +
342B GLN* 2.8 43.8 + - - +
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Residues in contact with ASN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B LYS 3.7 1.0 - - - +
305B TRP* 3.5 2.6 - - - -
306B TRP* 3.0 50.7 + - + +
328B TYR* 3.3 30.5 + - + +
329B ASP* 1.3 74.8 - - - +
331B VAL* 1.3 66.9 + - - +
332B GLU* 4.5 1.9 + - - +
339B LYS* 3.9 34.6 - - - +
340B ASN 3.3 3.6 + - - -
341B ASN* 3.7 14.6 + - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.6 24.2 - - + -
26B THR 3.9 7.4 - - - +
27B GLY* 3.8 18.2 - - - +
28B ALA* 3.6 16.4 - - + +
303B THR* 4.0 14.6 - - - -
304B LYS 3.5 7.4 - - - +
305B TRP* 3.7 20.0 - - + -
330B ASN* 1.3 81.3 + - - +
332B GLU* 1.3 63.2 + - - +
339B LYS* 3.2 1.1 - - - -
340B ASN* 2.6 41.1 + - + +
376B TRP* 3.2 21.0 + - + -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 3.4 4.5 - - - -
304B LYS* 2.9 62.7 + - + +
330B ASN* 4.3 2.6 + - - +
331B VAL* 1.3 77.1 - - - +
333B SER* 1.3 75.7 + - - +
334B GLN* 3.5 2.1 + - - -
337B GLY* 3.9 15.0 - - - +
338B ASP 3.3 11.0 - - - +
339B LYS* 2.9 37.6 + - + +
376B TRP* 4.2 0.4 - - - -
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B GLY 4.2 5.2 + - - -
332B GLU* 1.3 76.5 - - - +
334B GLN* 1.3 58.3 + - - +
335B ARG 3.0 14.9 + - - -
336B THR* 3.3 21.5 + - - -
337B GLY* 2.9 27.5 + - - -
338B ASP 3.0 8.8 + - - -
376B TRP* 3.5 33.3 - - - +
393B ALA* 3.2 22.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il